Have a look at this: http://tools.proteomecenter.org/wiki/index.php?title=TPP:Building_Windows-native_binaries_with_Mingw&printable=yes&printable=yes
On Thu, Jul 1, 2010 at 3:00 PM, Ronald W. Finnegan <[email protected]> wrote: > can you recommend a compiler that i can use to run makefile on a 64 > bit windows server? > > On Jul 1, 1:42 pm, Brian Pratt <[email protected]> wrote: >> You'll need to get the entire source tree from >> /sashimi/trunk/trans_proteomic_pipeline/ down, them cd to >> /sashimi/trunk/trans_proteomic_pipeline/src and "make _Mascot2XML". >> >> On Thu, Jul 1, 2010 at 9:58 AM, Ronald W. Finnegan <[email protected]> wrote: >> >> >> >> >> >> > I have downloaded the MascotConverter.cxx source file. >> >> > How do I compile the MascotConverter file so that the TPP source file >> > dependencies are met? >> >> > On Jul 1, 12:35 pm, Jimmy Eng <[email protected]> wrote: >> > >http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteom... >> >> > > This just points you to the Mascot2XML source files (which are >> > > dependent on other source files in the TPP project). >> >> > > On Thu, Jul 1, 2010 at 6:22 AM, Ronald W. Finnegan <[email protected]> >> > > wrote: >> >> > > > Jimmy, >> >> > > > I am using the Mascot2XML from the last TPP version released >> > > > 9-9-2009. Can you please point me to the trunk where I can download >> > > > rev 4945 from your April 15, 2010 check-in? >> >> > > > thanks >> >> > > > Ron >> >> > > > On Jun 30, 7:02 pm, Jimmy Eng <[email protected]> wrote: >> > > >> I have faint memories of dealing with this but I'm away from work so >> > > >> can't confirm. This might've been fixed in rev 4945 check-in on April >> > > >> 15th; my check-in log message for Mascot2XML was "parsing update for >> > > >> entry with protein n-term modification which doesn't seem to be >> > > >> handled by current code". >> >> > > >> Are you able to compile Mascot2XML from trunk and see if the problem >> > > >> goes away? Otherwise, I'll follow-up with this next week when I'm >> > > >> back at work. >> >> > > >> On Tue, Jun 29, 2010 at 5:59 AM, Ronald W. Finnegan >> > > >> <[email protected]> wrote: >> >> > > >> > Can anyone tell me if this bug reported back in April 2009 has been >> > > >> > fixed: >> >> > > >> > Thermo Orbitrap RAW file is inputted into tpp -> convert to mzxml -> >> > > >> > convert to mgf -> run mascot -> convert to pepXML >> >> > > >> > The problem is as follows: >> >> > > >> > When I use the mascot default modification Acetyl (protein N-term), >> > > >> > the TPP converter that converts the mascot output .DAT file to >> > > >> > pepXML >> > > >> > format creates the following header in the pepXML file: >> >> > > >> > <aminoacid_modification aminoacid=" " mass="42.010559" >> > > >> > massdiff="42.010559" peptide_terminus="n" variable="Y"/> >> > > >> > <aminoacid_modification aminoacid="N" mass="156.053486" >> > > >> > massdiff="42.010559" peptide_terminus="n" variable="Y"/> >> > > >> > <aminoacid_modification aminoacid="-" mass="42.010559" >> > > >> > massdiff="42.010559" peptide_terminus="n" variable="Y"/> >> > > >> > <aminoacid_modification aminoacid="t" mass="42.010559" >> > > >> > massdiff="42.010559" peptide_terminus="n" variable="Y"/> >> > > >> > <aminoacid_modification aminoacid="e" mass="42.010559" >> > > >> > massdiff="42.010559" peptide_terminus="n" variable="Y"/> >> > > >> > <aminoacid_modification aminoacid="r" mass="42.010559" >> > > >> > massdiff="42.010559" peptide_terminus="n" variable="Y"/> >> > > >> > <aminoacid_modification aminoacid="m" mass="42.010559" >> > > >> > massdiff="42.010559" peptide_terminus="n" variable="Y"/> >> >> > > >> > If you look at this header closely, the entries are not only >> > > >> > meaningless, but there is something funny to be seen if you look at >> > > >> > the aminoacid="" entries: >> >> > > >> > aminoacid=" " >> > > >> > aminoacid="N" >> > > >> > aminoacid="-" >> > > >> > aminoacid="t" = N - term >> > > >> > aminoacid="e" >> > > >> > aminoacid="r" >> > > >> > aminoacid="m" >> >> > > >> > as far as I know the aminoacid property should indicate aminoacid >> > > >> > letters and not be spelling out N-term. This is obviously a parsing >> > > >> > error occurring somewhere during the conversion. >> >> > > >> > Here is the link the original thread: >> >> > > >> >http://groups.google.com/group/spctools-discuss/browse_thread/thread/... >> >> > > >> > thanks >> >> > > >> > Ron >> >> > > >> > -- >> > > >> > You received this message because you are subscribed to the Google >> > > >> > Groups "spctools-discuss" group. >> > > >> > To post to this group, send email to >> > > >> > [email protected]. >> > > >> > To unsubscribe from this group, send email to >> > > >> > [email protected]. >> > > >> > For more options, visit this group >> > > >> > athttp://groups.google.com/group/spctools-discuss?hl=en.-Hidequoted >> > > >> > text - >> >> > > >> - Show quoted text - >> >> > > > -- >> > > > You received this message because you are subscribed to the Google >> > > > Groups "spctools-discuss" group. >> > > > To post to this group, send email to [email protected]. >> > > > To unsubscribe from this group, send email to >> > > > [email protected]. >> > > > For more options, visit this group >> > > > athttp://groups.google.com/group/spctools-discuss?hl=en.-Hide quoted >> > > > text - >> >> > > - Show quoted text - >> >> > -- >> > You received this message because you are subscribed to the Google Groups >> > "spctools-discuss" group. >> > To post to this group, send email to [email protected]. >> > To unsubscribe from this group, send email to >> > [email protected]. >> > For more options, visit this group >> > athttp://groups.google.com/group/spctools-discuss?hl=en.- Hide quoted text >> > - >> >> - Show quoted text - > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
